Detection, identification and quantitation of specific microorganisms is fundamental to many areas of microbiology ranging from the detection of pathogens in samples of human origin, to spoilage organisms or pathogens in food and beverages and environmental contaminants in municipal water. There are numerous examples where antibiotic treatment is instituted before the infectious agent has been confirmed, food is released for consumption before the microbiological test results are available, or municipal water is distributed via pipelines to the public while culture-based tests are still incubating. The requirement for rapid and accurate test results is obvious.
Comparative analysis of ribosomal RNA (rRNA) sequences or genomic DNA sequences corresponding to said rRNA (rDNA) has become a widely accepted method for establishing phylogenetic relationships between bacterial species (Woese, Microbiol. Rev. 51:221-271 (1987)), and Bergey's Manual of systematic bacteriology has been revised based on rRNA or rDNA sequence comparisons.
Ribosomal RNA or rDNA sequence differences between closely related species enable design of specific probes for microbial identification and thus enable diagnostic microbiology to be based on a single genetic marker rather than a series of phenotypic markers as characterizing traditional microbiology (Delong et al., Science 342:1360-1363 (1989)).
The taxonomy of the genus Pseudomonas has been changed in recent years, such that many species previously classified as Pseudomonas species have been reclassified and now belongs to other genera, such as Burkholderia, Xanthomonas, Aeromonas, Brevundimonas etc. However many current methods, such as Pseudomonas specific growth media, are still based on the former taxonomy, such the microorganisms identified as Pseudomonas (sensu stricto) in fact may be former Pseudomonas species not longer belonging to the Pseudomonas genus (Pacheco & Sage, Abstract, Annual Meeting of the American Society for Microbiology, Salt Lake City, May 2002). There is therefore a need for novel identification methods reflecting the revised taxonomy of the genus Pseudomonas. 
Despite its name, Peptide Nucleic Acid (PNA) is neither a peptide nor a nucleic acid, it is not even an acid. PNA is a non-naturally occurring polyamid that can hybridize to nucleic acid (DNA and RNA) with sequence specificity (See: U.S. Pat. No. 5,539,082) and Egholm et al., Nature 365:566-568 (1993)) according to Watson-Crick base paring rules. However, whereas nucleic acids are biological materials that play a central role in the life of living species as agents of genetic transmission and expression, PNA is a recently developed totally artificial molecule, conceived in the minds of chemists and made using synthetic organic chemistry. PNA also differs structurally from nucleic acid. Although both can employ common nucleobases (A, C, G, T, and U), the backbones of these molecules are structurally diverse. The backbones of RNA and DNA are composed of repeating phosphodiester ribose and 2-deoxyribose units. In contrast, the backbones of the most common PNAs are composed on (aminoethyl)-glycine subunits. Additionally, in PNA the nucleobases are connected to the backbone by an additional methylene carbonyl moiety. PNA is therefore not an acid and therefore contains no charged acidic groups such as those present in DNA and RNA. The non-charged backbone allows PNA probes to hybridize under conditions that are destabilizing to DNA and RNA. Attributes that enable PNA probes to access targets, such as highly structured rRNA and double stranded DNA, known to be inaccessible to DNA probes (See: Stephano & Hyldig-Nielsen, IBC Library Series Publication #948. International Business Communication, Southborough, Mass., pp. 19-37 (1997)). PNAs are useful candidates for investigation when developing probe-based hybridization assays because they hybridize to nucleic acids with sequence specificity. However, PNA probes are not the equivalent of nucleic acid probes in structure or function.
There is a need in the field for effective PNA probes that can be used to analyze Pseudomonas (sensu stricto) in a wide range of samples. PNA probes targeting Pseudomonas aeruginosa have previously been described (Stender et al., J. Microbiol. Methods 42:245-253 (2000), however the heterogenicity of the species within the genus Pseudomonas complicates the design of specific PNA probes targeting all species of the genus Pseudomonas. 